MethylMix

DOI: 10.18129/B9.bioc.MethylMix  

MethylMix: Identifying methylation driven cancer genes

Bioconductor version: Release (3.16)

MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.

Author: Olivier Gevaert

Maintainer: Olivier Gevaert <olivier.gevaert at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MethylMix")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MethylMix")

 

HTML	R Script	MethylMix
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, StatisticalMethod
Version	2.28.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 years)
License	GPL-2
Depends	R (>= 3.2.0)
Imports	foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest
LinkingTo
Suggests	BiocStyle, doParallel, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MethylMix_2.28.0.tar.gz
Windows Binary	MethylMix_2.28.0.zip (64-bit only)
macOS Binary (x86_64)	MethylMix_2.28.0.tgz
macOS Binary (arm64)	MethylMix_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MethylMix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethylMix
Bioc Package Browser	https://code.bioconductor.org/browse/MethylMix/
Package Short Url	https://bioconductor.org/packages/MethylMix/
Package Downloads Report	Download Stats